There are a couple different ways this might happen.
1. Your story doesn't stretch far enough.
Basically, this is when your idea that you thought was a novel or novella falls short. Usually by a lot, meaning several thousand words or more. Just keep in mind there's nothing wrong with writing a short story or a novelette. You probably won't be able to throw it up on Amazon by itself, but there are lots of venues still that do take short stories. Magazines, webzines, anthologies are all out there needing material and a lot of them do pay for them. Currently there are even some publishers that are willing to e-publish novella's.
2. Point of View
You may start wading into a piece working with who you feel should be the main character, only to discover far more interesting things are happening to someone else. This can be extremely difficult to deal with, as a lot of times, changing the point of view (POV) can mean going back and starting over from the very beginning, and nobody likes having work that seems like it was a waste of time. Here's the thing though, it wasn't a waste of time because it led you to a place where you could see the right path. Start over from the beginning if you need to, but keep that first piece handy to remind yourself of what was going on that leads you back to the other character in the first place. Maybe your story will work with a mixed POV, back and forth between the two characters. Or maybe you could turn that first piece into an extra short story, to give the readers something that adds further depth to the main storyline for those who want to know more.
3. False Starts.
You revved the engine, hit the gas, and you've made it through the first thousand words when the engine dies. It's not writer's block, it's not a bad story or one that falls short. Something is broken, though, and you're really not sure what. Maybe you've just lost interest in that first thousand words. Maybe you just can't see how to get from point A to point B. It could be that this particular story hasn't quite "marinated" long enough. There's nothing really wrong with the story, but the inspiration for the entire thing hasn't quite struck yet and it's not one that's going to let you force it through. This can be frustrating because it feels like writer's block, even though it's actually subtly different. After all, you have the idea, the energy, but it still won't come out. Like your fingers are frozen just above the keys. What can you do? Well, try reading everything you've done already on that story. Read it from the start, go over your notes, see if something jumps up waving and screaming at you. If that doesn't work, you may just have to accept that it's not the right time for that story yet and set it aside for a while. Busy yourself with other things, start a new piece, maybe even meditate on the issue. It's not giving up if you come back to it later on with a fresh mind.
The point I'm actually making here is that there are lots of reasons that a piece we're working on might stall out or not come out the way we anticipated. It can be extremely frustrating. It can also be temping to simply drag the files up into the Recycle bin and hit 'Delete'.
Just because something isn't working out NOW, doesn't mean you won't have that "Eureka!" moment later on, and of all the things I've listed, few are really as demoralizing as having that epiphany and then remembering that you'd deleted all the work you'd done, rendering that new moment of brilliance useless. Even if you end up never finishing a story, you have the start there to play with, twist and mold. Pull it out and poke at it sometimes just for the hell of it. It might turn into a completely different story, or give you ideas or characters for others pieces that might be floundering a bit. Inspiration can come from some interesting places sometimes, and it shouldn't surprise any writer that the key to making one story work might be built from the parts of a story that just never got off the ground.
So don't throw any of your broken works in the recycle bin. Throw them in the 'bits box' for later.